title: HEK R2 input

description:
HEK.Total.R2.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: HEK m6Aseq.xlsx

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files


title: T47D_mRNA_siCTRL_noSerum_3h_serum_readdition_rep2

status: Public on Nov 21 2019

type: SRA

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: RNA-seq pair end (PE)

library_source: transcriptomic

data_processing:
RNA-seq analysis.  (https://docs.google.com/document/d/1yRZevDdjxkEmda9WF5-qoaRjIROZmicndPl3xetFftY/edit?usp=sharing)
RNA-seq analysis. Differential expression (www.dropbox.com/s/026pc48kfuqr88g/RNA_analysis_deseq.2.R?dl=0)
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads.
To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads.

tag: cell line

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, followed by re-addition of 10% charcoal-treated (CT) FBS after the indicated time

tag: serum

value: serum-starved + charcoal-treated (CT) 3h


title: HEK R1 input

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

country: USA

institute: University of Chicago

description:
HEK.Total.R1.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: HEK m6Aseq.xlsx

molecule: polyA RNA

extract_protocol:
PAR-CLIP m6A-seq was performed on cells isolated using scraping. m6A-seq and RNAseq were performed on RNA isolated as follows. The nuclear and cytoplasmic fractions of postnatal day 11 (P11) Fmr1KO wild type mouse cortices were isolated using the NE-PER kit (ThermoFisher #78835) following manufacturer’s instructions. The nuclear and cytoplasmic fractions of HEK293T cells were isolated using the following procedure: 3 million HEK293T cells were lysed on ice for 5 minutes using 60μl of NP40 lysis buffer (0.075% Nonidet P40, 10 mM Tris-HCl (pH 7.5), 150mM NaCl, 1:100 cOmplete EDTA-free protease inhibitor (Roche), 1:100 superase inhibitor (ThermoFisher AM2694). The cell lysate was layered over 150μl of chilled sucrose cushion (24% RNase-free sucrose in NP40 lysis buffer) and centrifuged at 4°C for 10 minutes at 15,000g. The supernatant was collected as the cytoplasmic fraction. The pellet was rinsed four times with PBS and collected as the nuclear fraction. The total, cytoplasmic, and nuclear fractions RNA were extracted using Trizol, mRNA was further purified using either one round of the mRNA DIRECT kit (ThermoFisher #61012) and one round of the RiboMinus Eukaryotic kit v2 (ThermoFisher #A15015), or two rounds of the mRNA DIRECT kit. RNA-seq library preparation was performed with TruSeq stranded mRNA sample preparation kit (Illumina).
Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: genotype/variation

value: Wild-type


title: AD-CAB 1008

city: Waurn Ponds

first: Nima

last: Kamal

state: VIC

address: 75 Pigdons Rd

department: School of Medicine

country: Australia

institute: Deakin University

data_processing:
Samples performed using NovaSeq 600 Sequencing system
FASTQ format converted to .CSV using Linux, WinSCP and PuTTy software
Data with no reads were filtered using edgeR in R
Data were trimmed using edgeR in R with specifications of false discovery rate (FDR) values < 0.05
Pathways were found using PANTHER software
Genome_build: Ensembl genome browser 97
Supplementary_files_format_and_content: Data were generated using edgeR in R; that included fold change (FD), counts per million (CPM), p value and FDR value

source_name: Shoulder Capsule

growth_protocol: Adhesive capsulitis protocol

extract_protocol:
Total RNA extraction using Qiagen RNA
NuGen Universal Plus mRNA-Seq according to manufacturer' protocols (15 cycles of PCR). NovaSeq on 300 cycle flowcell generating 2x151 read length

treatment_protocol: RNAlater

tag: age

tag: Sex

value: Female


title: T47D_mRNA_siCTRL_noSerum_3h_serum_readdition_rep1

description: RNA-seq pair end (PE)


title: m273_ChIP-seq_LNCap -R GFP+pGIPZ shFoxA1

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: LNCap -R HA GFP+pGIPZ shFoxA1

library_source: genomic

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

molecule: genomic DNA

source_name: Prostate cancer cell line

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS or  5% charcoal-stripped serum

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated by using the indicated antibody.  DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer. Libraries were prepared according to Illumina's instructions.

treatment_protocol: LNCaP cells were co-infected with FoxA1 knockdown and FoxA1 WT or muatnts lentivirus and puro selected for 4-5 days, hormone starvation for 3 days, treat with or without 10nM R1881 for 16h before fixation by 1% paraformaldehyde.

value: LNCaP

tag: genotype

value: GFP+pGIPZ shFoxA1

tag: knockdown rna

tag: transfected with

value: GFP

tag: treatment

value: Ethanol

tag: antibody

value: HA

tag: vendor

value: Abcam

tag: catalog number

tag: lot/batch number


title: 293T cells, ETV7 -IFN C

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the human transcriptome (hg19) using STAR and the samples were run on Basespace (Illumina).
Mapped reads were normalized and averaged; fold change then calculated by comparing the interferon alpha treated samples to untreated samples.
Genome_build: hg19
Supplementary_files_format_and_content: bulkRNAseq_ETV7ifna293T_mapped.csv reports raw counts

source_name: 293T human kidney cell line

growth_protocol: 293T cells maintained throughout in complete growth media.

extract_protocol:
At 9 h post interferon treatment, cells were lysed and total RNA collected using the Monarch Total RNA Miniprep Kit (NEB).
mRNA was prepped for sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II RNA Library Prep Kit (NEB #E7770), and NEBNext Multiplex Oligos for Illumina (NEB #E7335, #E7500).

treatment_protocol: Cells were transfected with plasmids, incubated for 36 h, then treated or not with interferon alpha for 9 h before collection.

value: 293T human kidney cell line

tag: transfection

value: ETV7-expressing plasmid

value: no treatment


title: HEK.FMR1.parclipm6a

description:
HEK.FMR1.input
m6A-affinity purified RNA bound to FMRP.
Immunoprecipitated RNA
processed data file: PARCLIP m6Aseq.xlsx

data_processing:
Library strategy: PAR-CLIP + m6Aseq
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files

extract_protocol:
PAR-CLIP m6A-seq was performed on cells isolated using scraping. m6A-seq and RNAseq were performed on RNA isolated as follows. The nuclear and cytoplasmic fractions of postnatal day 11 (P11) Fmr1KO wild type mouse cortices were isolated using the NE-PER kit (ThermoFisher #78835) following manufacturer’s instructions. The nuclear and cytoplasmic fractions of HEK293T cells were isolated using the following procedure: 3 million HEK293T cells were lysed on ice for 5 minutes using 60μl of NP40 lysis buffer (0.075% Nonidet P40, 10 mM Tris-HCl (pH 7.5), 150mM NaCl, 1:100 cOmplete EDTA-free protease inhibitor (Roche), 1:100 superase inhibitor (ThermoFisher AM2694). The cell lysate was layered over 150μl of chilled sucrose cushion (24% RNase-free sucrose in NP40 lysis buffer) and centrifuged at 4°C for 10 minutes at 15,000g. The supernatant was collected as the cytoplasmic fraction. The pellet was rinsed four times with PBS and collected as the nuclear fraction. The total, cytoplasmic, and nuclear fractions RNA were extracted using Trizol, mRNA was further purified using either one round of the mRNA DIRECT kit (ThermoFisher #61012) and one round of the RiboMinus Eukaryotic kit v2 (ThermoFisher #A15015), or two rounds of the mRNA DIRECT kit. RNA-seq library preparation was performed with TruSeq stranded mRNA sample preparation kit (Illumina).
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

value: Overexpressing Flag-FMR1


title: m306_ChIP-seq_LNCap -R 253+pGIPZ shFoxA1

description: LNCap -R HA 253+pGIPZ shFoxA1

value: 253+pGIPZ shFoxA1


title: HEK.FMR1mut.parclipm6a

description:
HEK.FMR1mut.input
m6A-affinity purified RNA bound to FMRP I304N.
Immunoprecipitated RNA
processed data file: PARCLIP m6Aseq.xlsx

value: Overexpressing Flag-FMR1-I304N


title: T47D_mRNA_sGTF3C5_noSerum_rep1

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

value: serum-starved


title: m272_ChIP-seq_LNCap -R GFP+pGIPZ

description: LNCap -R HA GFP+pGIPZ

value: GFP+pGIPZ

value: pGIPZ


title: m292_ChIP-seq_LNCap +R 388+pGIPZ shFoxA1

description: LNCap +R HA 388+pGIPZ shFoxA1

value: 388+pGIPZ shFoxA1


title: AD-CAB 1007

value: Female


title: AD-CAB 1006


title: HEK.FMR1mut.parclip

description:
HEK.FMR1mut.IP
RNA bound to FMRP I304N.
Immunoprecipitated RNA
processed data file: PARCLIP m6Aseq.xlsx

data_processing:
Library strategy: PAR-CLIP
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files


title: m286_ChIP-seq_LNCap +R 266+pGIPZ shFoxA1

description: LNCap +R HA 266+pGIPZ shFoxA1

value: LNCaP

value: 266+pGIPZ shFoxA1


title: AD-CAB 1005


title: m274_ChIP-seq_LNCap -R WT+pGIPZ shFoxA1

description: LNCap -R HA WT+pGIPZ shFoxA1

value: WT+pGIPZ shFoxA1

value: WT

value: Ethanol


title: T47D_mRNA_siCTRL_noSerum_rep2

description: RNA-seq pair end (PE)


title: HEK.FMR1.parclip

description:
HEK.FMR1.IP
RNA bound to FMRP.
Immunoprecipitated RNA
processed data file: PARCLIP m6Aseq.xlsx


title: m311_ChIP-seq_LNCap +R 253+pGIPZ shFoxA1

description: LNCap +R HA 253+pGIPZ shFoxA1

value: HA

value: Abcam


title: T47D_mRNA_siCTRL_noSerum_rep1

description: RNA-seq pair end (PE)


title: m312_ChIP-seq_LNCap +R FENG+pGIPZ shFoxA1

description: LNCap +R HA FENG+pGIPZ shFoxA1

value: FENG+pGIPZ shFoxA1

value: FENG


title: AD-CAB 1009


title: AD-CAB 1004

value: Male


title: T47D_reserum_input

description: ChIP-seq single end (SE)

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). P-values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment.

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, then 10% FBS was adeed back for 30'

value: reserum

tag: chip-antibody


title: AD-CAB 1003


title: m285_ChIP-seq_LNCap +R 226+pGIPZ shFoxA1

description: LNCap +R HA 226+pGIPZ shFoxA1

value: 226+pGIPZ shFoxA1


title: T47D_mRNA_siGTF3C5_noSerum_24h_serum_readdition_rep1

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, followed by re-addition of 10% charcoal-treated (CT) FBS after the indicated time

value: serum-starved + charcoal-treated (CT) 24h


title: AD-CAB 1002


title: m289_ChIP-seq_LNCap +R 87+pGIPZ shFoxA1

description: LNCap +R HA 87+pGIPZ shFoxA1

value: 87+pGIPZ shFoxA1


title: AD-CAB 1001

value: Female


title: T47D_POL2_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

value: serum-starved

value: rabbit polyclonal antibody anti-Pol II Santa Cruz (N20) (sc-899)


title: m310_ChIP-seq_LNCap +R WT+pGIPZ shFoxA1

description: LNCap +R HA WT+pGIPZ shFoxA1

value: LNCaP

value: WT+pGIPZ shFoxA1

value: WT


title: T47D_POL2_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% FBS

value: non-serum starved


title: T47D_H3K18ac_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house rabbit polyclonal antibody anti-H3K18ac


title: m300_ChIP-seq_LNCap +R GFP+pGIPZ shFoxA1

description: LNCap +R HA GFP+pGIPZ shFoxA1

value: GFP+pGIPZ shFoxA1

value: GFP

value: HA

value: Abcam


title: m299_ChIP-seq_LNCap +R GFP+pGIPZ

description: LNCap +R HA GFP+pGIPZ

value: GFP+pGIPZ

value: pGIPZ


title: MCF10A_noSerum_input

description: ChIP-seq single end (SE)

value: DMEM/F12 supplied with 20 ng/ml epidermal growth factor, 0.5 ug/ml hydrocortisone, 10 ug/ml insulin, and 5% horse serum (with the addition of 100 ng/ml cholera toxin), then subjected to serum starvation (0% serum) for 16h


title: TTC1240_N106_SMARCB1_Empty_MNaseSeq

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq and Mnase-seq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq, ATACseq and Mnase-seq data, output BAM files were converted into BigWig track files using BEDTools and UCSC utilities in order to display coverage throughout the genome (in RPM).
For the RNAseq data, tracks were generated using the deepTools v2.5.3 bamCoverage function.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of RNA or DNA fragments across the genome in reads per million.

source_name: tumor cell line

growth_protocol: TTC1240 and G401 cells were grown in DMEM (Gibco, 11960-44), supplemented with 10% FBS, 1X GlutaMAX (Gibco, 35050-061), 100 U/mL penicillin-streptomycin (Gibco, 15140-122), 1mM sodium pyruvate (Gibco, 11360-070), 1X MEM NEAA (Gibco, 11140-050), 10 mM HEPES, 1X 2-mercaptoethanol. The SMARCB1^K364del/+ iPSC cells were maintained in StemFlex Medium (Gibco) prior to differentiation. At Day (-2) of NGN2-mediated differentiation, the iPSCs were washed with 1X PBS (Gibco), and dissociated using Accutase (Innovative Cell Technologies).

extract_protocol:
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. All ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. RNA was collected in biological duplicate using the RNeasy Mini Kit (QIAGEN). All RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. ATAC-seq libraries were prepared in biological replicates using standard protocol (Buenrostro et al., Current Protocols (2013)) with 12 cycles of amplification. ATAC-seq samples were sequenced on Nex-seq 500 using 37 bp, 37 bp pair-end sequencing parameters.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). TTC1240 and G401 cells were lentivirally infected with either Empty vector, or one of four SMARCB1 variant constructs (full length, K364del, R377H, or delCC construct) for 48h and then selected with blasticidin for 5 days. Cells were harvested 7 days post-infection. Treatment: The SAH iPSC cell line underwent CRISPR/Cas9 mediated genome editing with a short-guide RNA (sgRNA) targeting exon 9 of the SMARCB1 gene and a single-stranded oligodeoxynucleotide (ssODN) donor strand encoding for the SMARCB1 K364del in-frame deletion. Cells were single cell sorted, genotyped and then confirmed via standard TA-cloning procedures to onbtain a SMARCB1+/+ WT control and K364del hetorzygous mutant (SMARCB1^K364del/+). The SMARCB1^K364del/+ iPSC cells were made into stable lines via lentiviral infection with either Empty vector or full-length SMARCB1 followed by blasticidin selection. Ngn2 differentiation of SAH cells: At Day (-2) cells were split and plated at 2K/well in geltrex coated plates. To induce NGN2-mediated differentiation, cells were infected with NGN2 lentiviral construct conjugated with EGFP and rTTA cassette on Day (-1). Media was changed periodically according to standard protocol.

tag: ngs approach

value: MNase-seq

tag: experimental condition

value: lentivirus:SMARCB1 Empty


title: TTC1240_N106_SMARCB1_FL_MNaseSeq

tag: cell line

value: lentivirus:SMARCB1 FL


title: TTC1240_N106_SMARCB1_K364del_MNaseSeq

value: lentivirus:SMARCB1 K364del


title: NV_GB_M3_2

city: Gainesville

first: Pablo

middle: Emiliano

last: Canton

state: Florida

address: Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

data_processing:
Low quality tiles removed from raw reads with FiltByTile script from BBMapSuite with d=0.75, qd=1,ed=1, va=0.5,qa=0.5,ea=0.5 parameters
Reads quality filtered and adapter trimmed with TrimGalore v 0.4.4
de novo assembly with Trinity v 2.8.3  with minimum kmer coverage of 2 and maximum read coverage of 200
Read mapping to reference transcriptome with Salmon v 0.12 with -gcBias flag
Salmon sf files imported into DESeq2 through TxImport package v 1.8.0 with -lengthScaledTPM parameter and not summarized to gene level
Differential transcript expression obtained through DESeq2 v 1.20.0 with apeglm shrinkage and lfc Threshold of -1/1
Genome_build: Nviridula.fasta
Supplementary_files_format_and_content: Flat text abundance estimation tables from DESeq2 for samples loaded for each model construction

organism: Nezara viridula

source_name: midgut M3

growth_protocol: insects were kept at 65% relative humidity and 27 +/- 1 C with 16:8 light:dark cycle

extract_protocol:
Tissue were dissected in PBS 0.1M pH 7.4, and then collected in RNA-later. For processing, all RNA-later was removed and total RNA was extracted through Ambion PureLink RNA extraction kit according to manufacturer’s instructions. Eluted RNA was treated with DNAse I for 30 min. Reactions were cleaned up by overnight precipitation at -20 C with isopropanol and sodium acetate pH 3.2. After centrifugation, pellet was washed with 70% Ethanol in Rnase free water, and final pellet resuspended in Rnase free water.
Sequencing facility prepared mRNA libraries by standard Illumina protocols

treatment_protocol: Upon molting to adults, insects were transferred to fresh corresponding diet and allowed to feed for a further 24 hours before dissection

tag: diet

value: green bean

tag: replicate

value: adult


title: NV_GB_M3_3

tag: age


title: lncRNA-3

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

country: China

institute: Chinese Academy of Agricultrual Sciences

description: LncRNA

data_processing:
Alignment: HiSAT2 using default settings; expression levels: StringTie v1.34d using default settings
Genome_build: genome de novo assembled in this study. The genome was submitted to NCBI under BioProject PRJNA505414. The .gff and .fasta file for transcript coordinates and sequence are available on the SuperSeries page.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Mesostigma viride

source_name: Cells

growth_protocol: The cells were cultivated in medium C in 250-ml Erlenmeyer flasks with gentle agitation at 23°C under the light:dark cycle of 10:14h and light intensity of 50 µmol photons·m-2·s-1.

extract_protocol:
Total RNA was extracted using the RNeasy Plus mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies) and rRNA removal using the Ribo-Zero kit (Epicenter) according to the manufacturer’s instructions. RNA integrity and centralization were detected using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
The resulting RNA samples were then used as input for library construction using the dUTP method. Three biological replicates without particular treatment were designed for lncRNA sequencing. RNA libraries were then sequenced on the Illumina HiSeq x10 with paired end 150 bp read length.

tag: strain


title: MCF10A_BDP1_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

tag: media

tag: serum

value: serum-starved

value: in house anti-BDP1 rabbit polyclonal


title: Sample 24_exvivo_PNT_S3_gd

city: Brussels

first: David

last: Vermijlen

address: Boulevard de Triomphe, accès 2 (CP205/3)

country: Belgium

institute: Université Libre de Bruxelles

description: processed data file: CPM_FT_PNT.csv

data_processing:
Approximately 30 million paired-end reads (2x101 bases) /sample were collected on a NovaSeq 6000 (Illumina)
Paired-end reads with variable trimming (minimum size 36 bases) were mapped against the human reference genome (GRCh38) using STAR_2.5.3a software to generate read alignments for each sample. Annotations Homo_sapiens.GRCh38.90.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq, followed by a library size normalization data processing step
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file include CPM (count per million) values for each Sample.

growth_protocol: Only for samples 1-12: Isolated HSPC (CD34+ cells) were seeded in a 6-well culture plate (5x105 cells/well) containing a monolayer of OP9DL1 cells in MEMα (Minimum Essential Medium α) supplemented with 20% fetal bovine serum, 1% NEAA, 1% Glutamine, 1% Pen/Strep in the presence of 10 ng/ml IL-7,10 ng/ml Flt3L and 5 ng/ml SCF. Every 4-5 days cells were harvested by vigorous pipetting and transferred in a new 6-well plate (between 5x105-1x106 cells/well). This in vitro system allow the generation of T cells. After ca. 30 days in co-culture with OP9DL1 cells, HPSC-derived γẟ T cells were stained and sorted on a FACS Aria III cell sorter, snap frozen in liquid nitrogen and stored at -80 °C for later RNA extraction.

extract_protocol:
RNA was extracted using RNeasy Plus Micro kit according to manufacturer’s instructions
Library was obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer's instruction

value: 1 year

tag: tissue/cell type source

value: Thymus

tag: cell type

value: gamma delta thymocytes

tag: cell subset


title: Sample 23_exvivo_PNT_S2_gd

description: processed data file: CPM_FT_PNT.csv

value: 4 months


title: lncRNA-2

description: LncRNA


title: T47D_TFIIIC_reserum

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, then 10% FBS was adeed back for 30'

value: reserum

value: in house anti-GTF3C2 rabbit polyclonal


title: NV_GB_M3_1


title: T47D_mRNA_sGTF3C5_noSerum_rep2

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h


title: RABV-SK-3

type: RNA

city: NANJING

first: SENLIN

last: JI

state: Jiangsu

address: No. 1, Weigang Road

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
RABV-SK3.txt(normalized)
Gene expression in human neuroblastoma cells infected with rabies virus

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60Â°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human lncRNA (4*180K Design ID 076500)  for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies, USA) was used to analyze the acquired array images. Agilent GeneSpring GX software package (version 13.1, Agilent Technology, USA) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were then identified through fold change.

source_name: SK-N-SH_RABV infected

label_protocol: Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human neuroblastoma cell line SK-N-SH was purchased from ATCC (stock number HTB-11). Cells were cultured at 37°C with 5% CO2 in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% fetal bovine serum (FBS) (Gibco/Invitrogen, Carlsbad, CA, USA). All media were supplemented with penicillin (100 U/ml) and streptomycin (100 g/ml).

extract_protocol: Total cellular RNA was isolated from the cells following the TRIzol reagent (Invitrogen) manufacturer's protocol. A NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, United States) and an Agilent 2100 (Agilent Technologies, California, United States) were used to determine RNA yield. RNA was subjected to agarose gel electrophoresis and ethidium bromide staining to evaluate RNA integrity. Only samples with OD260/OD280 ratios between 1.8 and 2.1, and OD260/OD230 ratios >1.8, were acceptable. Samples were also required to be free of genomic DNA contamination and have a 28S/18S band intensity ratio greater than 2.0, as determined by staining after electrophoresis.

treatment_protocol: Cells at 70 to 80% confluency in 6-well plates were rinsed twice with PBS, followed by the addition of diluted RABV (MOI = 1). After incubation for 1 hour at 37°C, the supernatant was discarded. The cells were then washed twice with PBS, and complete medium was added. After 24 h, infected cells were harvested and lysed in 1 mL of TRIzol reagent (Invitrogen)

value: SK-N-SH

value: human neuroblastoma cells

tag: treatment

value: rabies virus (RABV) infected


title: RABV-SK-1

description:
RABV-SK1.txt(normalized)
Gene expression in human neuroblastoma cells infected with rabies virus


title: RABV-SK-2

description:
RABV-SK2.txt(normalized)
Gene expression in human neuroblastoma cells infected with rabies virus


title: RABV-NON-SK-3

description:
RABV-NON-SK3.txt(normalized)
Gene expression in human neuroblastoma cells

value: uninfected


title: RABV-NON-SK-2

description:
RABV-NON-SK2.txt(normalized)
Gene expression in human neuroblastoma cells


title: RABV-NON-SK-1

description:
RABV-NON-SK1.txt(normalized)
Gene expression in human neuroblastoma cells


title: lncRNA-1

description: LncRNA


title: MCF10A_TFIIIC_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: DMEM/F12 supplied with 20 ng/ml epidermal growth factor, 0.5 ug/ml hydrocortisone, 10 ug/ml insulin, and 5% horse serum (with the addition of 100 ng/ml cholera toxin), then subjected to serum starvation (0% serum) for 16h


title: MCF10A_serum_input

description: ChIP-seq single end (SE)

value: DMEM/F12 supplied with 20 ng/ml epidermal growth factor, 0.5 ug/ml hydrocortisone, 10 ug/ml insulin, and 5% horse serum (with the addition of 100 ng/ml cholera toxin)

value: non-serum starved


title: smallRNA-3

description: Small RNA

data_processing:
Raw small-RNA-seq reads with single end 50 bp read length from Illumina HiSeq x10 were trimmed to remove 3′-adapters and filtered for quality control and trimmed length ≥ 16 nucleotides using cutadapt v1.9.1 with the settings “-a TGGAATTCTCGGGTGCCAAGG –discard-untrimmed -m 18 –max-n =0”. All clean reads were filtered by removing the sequences smaller than 18 nt or longer than 30 nt. Alignment: bowtie using default settings; expression levels: miRDeep2 using default settings
Genome_build: genome de novo assembled in this study. The genome was submitted to NCBI under BioProject PRJNA505414. The .gff and .fasta file for transcript coordinates and sequence are available on the SuperSeries page.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

extract_protocol:
Small RNA was extracted using the mirPremier microRNA Isolation Kit (Sigma-Aldrich) according to the manufacturer’s protocol.
small-RNA-seq libraries were constructed using the NEBnext small-RNA library kit (NEB), following the manufacturer’s instructions.


title: NV_GB_M2_3

source_name: midgut M2

value: green bean

value: adult


title: NV_GB_M2_1


title: MCF10A_POL3_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: serum-starved

value: in house anti-POL3 rabbit polyclonal


title: Sample 22_exvivo_PNT_S1_gd

description: processed data file: CPM_FT_PNT.csv

value: 8 years

value: Thymus

value: gamma delta thymocytes


title: Sample 21_exvivo_FT_S3_gd

description: processed data file: CPM_FT_PNT.csv

value: 17 weeks


title: NV_GB_M1_2

source_name: midgut M1


title: smallRNA-1

description: Small RNA


title: MCF10A_BDP1_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house anti-BDP1 rabbit polyclonal


title: NV_GB_M2_2


title: RNA-seq_High temperature rep1

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to M. viride genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters. Differentially expressed genes (DEGs) were identified by DEseq2 package, and only transcripts with fold change ≥ 2 and FDR ≤ 0.01 were considered as DEGs.
Genome_build: genome de novo assembled in this study. The genome was submitted to NCBI under BioProject PRJNA505414. The .gff and .fasta file for transcript coordinates and sequence are available on the SuperSeries page.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies). Samples were then subjected to poly(A) purification using oligo-dT beads (Life Technologies) followed by rRNA removal using Ribo-Zero Kit (Epicenter) according to the manufacturer’s instructions. RNA integrity was measured using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
Library construction were done using TruSeq® Stranded mRNA Library Prep Kit following the manufacturer’s instructions (Illumina). 16 paired-end libraries were constructed and sequenced according to the Illumina HiSeqTM platform sequencing protocols.


title: Sample 17_exvivo_PNT_S2_ab

description: processed data file: CPM_FT_PNT.csv

value: 4 months

value: alpha beta thymocytes


title: MCF10A_TFIIIC_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: in house anti-GTF3C2 rabbit polyclonal


title: T47D_TFIIIC_noSerum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h


title: smallRNA-2

description: Small RNA


title: Sample 19_exvivo_FT_S1_gd

description: processed data file: CPM_FT_PNT.csv

value: 19 weeks


title: NV_GB_M1_3


title: MCF10A_POL3_Serum_ChIP-seq

description: ChIP-seq single end (SE)


title: Sample 18_exvivo_PNT_S3_ab

description: processed data file: CPM_FT_PNT.csv

value: 1 year


title: Sample 20_exvivo_FT_S2_gd

description: processed data file: CPM_FT_PNT.csv


title: RNA-seq_High temperature rep2


title: NV_GB_M1_1


title: RNA-seq_Low pH rep1


title: RNA-seq_Low pH rep2


title: T47D_TFIIIC_Serum_ChIP-seq

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% FBS


title: Sample 16_exvivo_PNT_S1_ab

description: processed data file: CPM_FT_PNT.csv


title: NV_GB_SG_3

source_name: salivary glands


title: Sample 15_exvivo_FT_S3_ab

description: processed data file: CPM_FT_PNT.csv


title: RNA-seq_High pH rep2


title: NV_GB_SG_2


title: Sample 14_exvivo_FT_S2_ab

description: processed data file: CPM_FT_PNT.csv


title: NV_GB_SG_1


title: RNA-seq_High pH rep1


title: RNA-seq_High light rep2


title: NV_C_M3_3

description:
abundance_corn_table.txt
abundance_midguts_table.txt

value: corn


title: RNA-seq_High light rep1


title: Sample 12_OP9DL1_Control_S3

description: processed data file: CMP_OP9DL1.csv

value: Term delivery

value: Hematopoietic stem and progenitor cells (HSPC)

value: gamma delta T cells (HSPC derived)


title: NV_C_M3_2

value: adult


title: NV_C_M3_1


title: Sample 11_OP9DL1_Control_S2

description: processed data file: CMP_OP9DL1.csv


title: RNA-seq_Darkness rep2


title: RNA-seq_Darkness rep1


title: Sample 10_OP9DL1_Control_S1

description: processed data file: CMP_OP9DL1.csv


title: Sample 9_OP9DL1_Lin28b_S3

description: processed data file: CMP_OP9DL1.csv


title: Sample 8_OP9DL1_Lin28b_S2

description: processed data file: CMP_OP9DL1.csv


title: Act5C-G4; dLsd1 RNAi_rep2

city: Toulouse

first: Luisa

last: Di Stefano

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative (CBI)

description: gene expression upon dLsd1 depletion by RNAi

hyb_protocol: The slides (Drosophila Gene Expression Microarray, 4x44K ref 021791) were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent)

scan_protocol: The slides were scanned on a Tecan MS200 scanner.

data_processing: The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The data from all the microarrays were transformed in log2 intensity. Then they were normalized together using the “limma” package function “normalizeQuantiles” and the “quantile” method. Normalization of the data was performed using the Bioconductor packages (http://www.bioconductor.org) and R software v3.1.2.

organism: Drosophila melanogaster

source_name: ovaries

label_protocol: The labeling was done using the Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: Flies were raised at 25°C, 70% humidity on standard Drosophila medium

extract_protocol: Total RNA was extracted from three independent preparations from Drosophila ovaries (2 days on yeast) using 500 µl Trizol (Invitrogen). RNA was treated with DNA-free™ DNA Removal Kit (Ambion) for 30 minutes at 37°C as described by the manufacturer

tag: genotype

value: Act5C-G4; dLsd1 RNAi

tag: gender

value: female


title: NV_C_M2_1


title: Act5C-G4_rep1

description: gene expression


title: Act5C-G4_rep3

description: gene expression


title: Sample 13_exvivo_FT_S1_ab

description: processed data file: CPM_FT_PNT.csv

value: Thymus


title: RNA-seq_Control2 rep1


title: Sample 7_OP9DL1_Lin28b_S1

description: processed data file: CMP_OP9DL1.csv


title: NV_C_M1_3


title: RNA-seq_Control1 rep2


title: Sample 6_OP9DL1_AB_S3

description: processed data file: CMP_OP9DL1.csv


title: RNA-seq_Control1 rep1


title: Act5C-G4; dLsd1 RNAi_rep3


title: NV_C_M2_3


title: p53 and Wdr5 DKO; hWDR5iRescue T48h, EB6 (rep-1)

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

description: Dox inducible HA-hWDR5 at T48h

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality using Trim Galore! v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), powered by CutAdapt v1.8.1 (http://dx.doi.org/10.14806/ej.17.1.200) and FastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Paired-end reads were aligned using Bowtie2 (v2.2.9) mm10 and only reads mapped in proper pair were included by samtools (v1.4). Non-uniquely mapping reads and reads mapped to chrM, chrX or chrY were excluded.  Any candidate reads of PCR duplicates were removed by samtools (v1.4).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to centre the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v2.1.1.20160309) with a threshold of FDR-corrected P < 1 × 10−2 using the Benjamini–Hochberg procedure for multiple hypothesis correction.
As called peaks may be caused by noise in the assay and not reflect true chromatin accessibility, we calculated an irreproducible discovery rate (IDR) for all pairs of replicates across a cell type. The IDR is an estimate of the threshold where two ranked lists of results, in this case peak calls ranked by P value, no longer represent reproducible events. Using this measure, we excluded peaks that were not reproducible (IDR < 5 × 10−3) across at least one pair of replicates in each cell type.
The bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from filtered BAM files by using “bamCoverage” from deepTools with parameters “--outFileFormat bigwig --ignoreDuplicates --normalizeUsingRPKM --minMappingQuality 30  --binSize 50 --Offset 5 -1”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

organism: Mus musculus

source_name: embryoid bodies

growth_protocol: Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
5x104 cells were used for transpoistion at 37C for 30 min using Illumina Nextera DNA Library Prep Kit.
Libraries were prepared with the Illumina Nextera DNA Library prep kit according to the manufacturer’s protocol.

treatment_protocol: 2% matrigel added at EB day 1. Dox was added at T12h or T48h in hWDR5 inducible groups.

tag: tissue

value: embryoid bodies

value: Embryonic stem cell Rx:GFP KI

value: p53 andWdr5 DKO, hWDR5 T48h rescue


title: Sample 4_OP9DL1_AB_S1

description: processed data file: CMP_OP9DL1.csv


title: RNA-seq_Cold rep2


title: p53 and Wdr5 DKO; hWDR5iRescue T12h, EB6 (rep-1)

description: Dox inducible HA-hWDR5 at T12h

value: p53 andWdr5 DKO, hWDR5 T12h rescue


title: NV_C_M2_2


title: RNA-seq_Control2 rep2


title: NV_C_SG_3

description:
abundance_corn_table.txt
abundance_glands_table.txt


title: KO non-TFR

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

description: Gene expression data from non-TFR cells from immunized KO mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST Array. GeneChips were washed and fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: non-TFR sorted from KO mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

extract_protocol: RNA was prepared with the RNeasy plus micro kit according to the manufacturer’s instructions (Qiagen).

tag: genotype/variation

value: Prdm1fl/flFoxP3YFP-Cre (KO)

value: non-TFR Treg


title: WT non-TFR

description: Gene expression data from non-TFR cells from immunized WT mice

source_name: non-TFR sorted from WT mice

value: FoxP3YFP-Cre (WT)


title: NV_C_M1_1


title: Act5C-G4; dLsd1 RNAi_rep1


title: WT TFR

description: Gene expression data from TFR cells from immunized WT mice

source_name: TFR sorted from WT mice

value: TFR


title: KO TFR

description: Gene expression data from TFR cells from immunized KO mice

source_name: TFR sorted from KO mice


title: NV_C_M1_2


title: RNA-seq_Cold rep1


title: Sample 3_OP9DL1_FL_S3

description: processed data file: CMP_OP9DL1.csv

value: 17 weeks


title: 5mC-2

data_processing:
Raw sequencing data were processed to filter out reads containing adapters by cutadapt v1.9.1 and low quality bases. Low-quality reads included two types: 1) Unknown bases are more than 10 %; 2) The ratio of bases whose quality was less than 20 was over 10 %. The clean sequences were then aligned to the reference genome using the Bismark aligner (v0.18.2) under the parameters (-N 1 ,-L 20, --bowtie2). Methylated cytosines were extracted from aligned reads using the Bismark methylation extractor with default parameters
Genome_build: genome was De novo assembled in this study and submitted to NCBI under BioProject PRJNA505414.
Supplementary_files_format_and_content: gff file contains information of each methylcytosine site

extract_protocol:
The M. viride cells were lysised in lysis buffer (50 mM, Tris-HCl pH8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1% PVP4000, 1mg/ml proteinase K) and genomic DNA for library was extracted using DNeasy Plant Mini Kit (QIAGEN).
M. viride DNA was sheared to approximately 250 bp fragments by sonication using a Bioruptor (Diagenode). The fragments were treated with end-repair, A-tailing and ligation of methylated Illumina adapters (Illumina) using KAPA’s Illumina library creation kit (KAPA Biosystems) according to the manufacturer’s instructions. The adaptor-ligated DNA was bisulfite-treated using EZ DNA Methylation Lightning Kit (Zymo Research), converting the nonmethylated nucleotides from cytosine to uracil. Lambda-phage genomic DNA was used as a negative control to determine the efficiency of the sodium bisulfite conversion reaction. Products were purified using QIAquick Gel Extraction kit (Qiagen) and amplified with ten cycles of PCR. DNA libraries were constructed according to the Epitect whole-genome bisulfite sequencing workflow (Illumina), and quantified using qPCR


title: NV_C_SG_2

value: corn


title: Wdr5 KO; hWDR5iRescue T48h, EB6 (rep-1)

description: Dox inducible HA-hWDR5 at T48h

value: Wdr5 KO, hWDR5 T48h rescue


title: Act5C-G4_rep2

description: gene expression


title: Wdr5 KO; hWDR5iRescue T12h, EB6 (rep-1)

description: Dox inducible HA-hWDR5 at T12h

value: Wdr5 KO, hWDR5 T12h rescue


title: Sample 2_OP9DL1_FL_S2

description: processed data file: CMP_OP9DL1.csv

value: 15 weeks

value: Hematopoietic stem and progenitor cells (HSPC)

value: gamma delta T cells (HSPC derived)


title: 5mC-1


title: Sample 1_OP9DL1_FL_S1

description: processed data file: CMP_OP9DL1.csv

value: 21 weeks


title: Sample 5_OP9DL1_AB_S2

description: processed data file: CMP_OP9DL1.csv


title: WT, EB6 (rep-1)

value: WT


title: MDA-MB-231_tet-shRNA5_no dox 8 days_2

status: Public on Nov 20 2019

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

institute: KU Leuven

data_processing:
Reads were mapped on hg38 human genome with gencode v22 as gene annotation using STAR
Read counts were normalized by calculating TPM (Transcripts Per Kilobase Million)
gene expression were quantified using RSEM v1.3.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene expression/splicing values for each sample

source_name: Triple-negative breast cancer cell line

growth_protocol: MCF10A cells were cultured in MEBM media (Lonza) supplemented with BPE, hEGF, insulin, hydrocortisone (Lonza, Bulletkit), 50 µg cholera toxin (Sigma) and 1% Pen/Strep. MDA-MB-231 cells were cultured in high glucose DMEM (Thermofisher), supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Cells were trypsinized, peletted, and RNA was harvested using Nucleospin (Macherey). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF10A cells were transfected with GapmeRs (Exiqon) designed against the candidate lncRNA or a scramble GapmeR using Lipofectamine 2000 (Thermofisher). The cells were cultured in a 1% O2 hypoxic chamber. MDA-MB-231 cells were used to create a stable cell line expressing three tetracycline inducible shRNAs against the candidate lncRNA and two constitutive shRNAs against SART3. shRNA induction of the tetracycline inducible shRNAs was accomplished by treating the cells with doxycycline (1µg/µl) for 48 hours or 8 days, refreshing doxycycline every 48h.

tag: shRNA


title: MDA-MB-231_tet-shRNA5_no dox 8 days_1


title: MDA-MB-231_tet-shRNA5_no dox 8 days_3


title: MDA-MB-231_tet-shRNA5_dox 8 days_3

tag: agent

value: DOX


title: MDA-MB-231_tet-shRNA5_dox 8 days_2

tag: cell line


title: MDA-MB-231_tet-shRNA4_dox_8 days_3


title: MDA-MB-231_tet-shRNA4_dox_8 days_2


title: MDA-MB-231_tet-shRNA4_no dox 8 days_2


title: MDA-MB-231_tet-shRNA5_dox 8 days_1


title: MDA-MB-231_tet-shRNA4_dox_8 days_1


title: MDA-MB-231 shGFP_2

value: shGFP


title: MDA-MB-231 shGFP_1


title: MDA-MB-231 shGFP_3


title: NV_C_SG_1

tag: diet

value: adult


title: MDA-MB-231_tet-shRNA4_no dox 8 days_1


title: MDA-MB-231 sh2_SART3_3


title: MDA-MB-231 sh2_SART3_1


title: MDA-MB-231 sh2_SART3_2


title: MDA-MB-231 sh3_SART3_3


title: MDA-MB-231 sh3_SART3_2


title: MOLM14.ASLAN_2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
AML MOLM14 cell line treated with ASLAN003, replicate 2.
processed data file: JB.Aslan_fpkmlg2.txt

data_processing:
bcl2fastq 2.17.1.14 was used for basecalling.
Sequenced reads were mapped to hg38 using STAR v2.4.2a with default parameters settings.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM v1.2.25 and Gencode v24 annotation.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: JB.Aslan_fpkmlg2.txt Tab-delimited text file includes FPKM values for each sample.

source_name: AML cell line

growth_protocol: KG-1 and MOLM-14 cells were grown in RPMI1640 (Biowest, France) supplemented with 10% of fetal bovine serum (FBS, Biowest) in a humid incubator with 5% CO2 at 37ºC.

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries, using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: KG-1 and MOLM-14 cells were treated with either DMSO or ASLAN003 for 96h. Each treatment was triplicated.


title: MOLM14.ASLAN_1

description:
AML MOLM14 cell line treated with ASLAN003, replicate 1.
processed data file: JB.Aslan_fpkmlg2.txt


title: MOLM14.DMSO_2

description:
AML MOLM14 cell line treated with DMSO, replicate 2.
processed data file: JB.Aslan_fpkmlg2.txt

value: DMSO


title: KG-1.ASLAN_2

description:
AML KG-1 cell line treated with ASLAN003, replicate 2.
processed data file: JB.Aslan_fpkmlg2.txt


title: MOLM14.DMSO_3

description:
AML MOLM14 cell line treated with DMSO, replicate 3.
processed data file: JB.Aslan_fpkmlg2.txt


title: KG-1.ASLAN_1

description:
AML KG-1 cell line treated with ASLAN003, replicate 1.
processed data file: JB.Aslan_fpkmlg2.txt


title: KG-1.ASLAN_3

description:
AML KG-1 cell line treated with ASLAN003, replicate 3.
processed data file: JB.Aslan_fpkmlg2.txt


title: MDA-MB-231_tet-shRNA4_no dox 8 days_3


title: KG-1.DMSO_2

description:
AML KG-1 cell line treated with DMSO, replicate 2.
processed data file: JB.Aslan_fpkmlg2.txt


title: KG-1.DMSO_3

description:
AML KG-1 cell line treated with DMSO, replicate 3.
processed data file: JB.Aslan_fpkmlg2.txt


title: KG-1.DMSO_1

description:
AML KG-1 cell line treated with DMSO, replicate 1.
processed data file: JB.Aslan_fpkmlg2.txt


title: MDA-MB-231 sh3_SART3_1


title: MOLM14.DMSO_1

description:
AML MOLM14 cell line treated with DMSO, replicate 1.
processed data file: JB.Aslan_fpkmlg2.txt


title: IU501

city: Indianapolis

first: Robert

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

description: C57BL/10 male mouse spleens were separated into CD19+ (B cells) and CD19- (T cells) cells using AutoMacs computer-controlled magnetic cell sorter (Miltenyi Biotec) using Gentle Macs mSpleen 4.01 program.

data_processing:
trim_galore! Adaptor and low quality trimming
STAR genome mapping to mm10 genome
featureCounts gene-level quantitation
edgeR differential expression analysis
data processing step
Genome_build: mm10
Supplementary_files_format_and_content: CPM, counts

source_name: splenic CD19+ isolated cells

growth_protocol: Cells (1×106 per ml) were then resuspended in 6 well plates in a total volume of 4 ml, and incubated for 3 h 37C in 5% CO2 incubator. Conditions included media (RPMI 1640 (Invitrogen) containing 10% heat-inactivated FBS (HyClone) and 1% penicillin/streptomycin, 1% glutamine (Invitrogen) with20mM HEPES pH 7.5 ).

extract_protocol:
After 3 h, cells were centrifuged and cell pellet was lysed in 700 μL Trizol (Thermo-Fisher) for RNA preparation. A time zero sample was also collected and lysed in Trizol. Three independent experiments were completed and analyzed separately. RNA was purified using the Direct-Zol Mini Prep RNA Isolation Kit (Zymo R2052) with DNaseI on-column treatment.
Approximately 500ng of each total RNA was converted into a sequencing library using the TruSeq mRNA Strand Specific Library Prep kit from Illumina, and 1x150 base single end reads were collected on an Illumina HiSeq V4/4000 instrument at the University of Colorado Genomics Core. Each total RNA sample (7 experimental conditions; 3 biological replicates) generated library was individually bar-coded, all the libraries were mixed and sequence data collected over 3 lanes.

treatment_protocol: Media plus 5mM HOAc, or media plus 5mM HOAc with either 200 μg/ml col(I), 200 μg/ml col(V), 10 μg/ml LPS (E. coli 0111:B4 (Sigma L4391), or 10 μg/ml goat anti-mouse F(ab’)2 anti-IgM (Jackson ImmunoResearch 115-006-075). Purified col(I) and col(V) were soluble in 50mM or 100mM HOAC, respectively, so the culture media had 20mM HEPES pH 7.5 added to restore the pH to neutrality.

value: Time Zero (Cell Separation)

tag: replicate

tag: Sex

value: male


title: IU403

value: HOAc

tag: strain


title: IU406

value: LPS+HOAc


title: IU506


title: IU407

value: anti-IgM+HOAc


title: IU503


title: IU404


title: IU504


title: IU402

value: No Treatment (3hr 37C culture)


title: IU405


title: IU505


title: IU507


title: IU401


title: IU307


title: IU305


title: IU304


title: IU306


title: IU303


title: WT_SeV

city: Bunkyo-ku

first: Kumiko

last: Ui-Tei

state: Tokyo

country: Japan

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy-3 labeled RNAs were fragmented by Gene Expression Hybridization kit (Agilent Techinologies) and hybridized to SurePrint G3 Human GE microarray ver.3 (Agilent Techinologies) at 65°C for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing: Signals were quantified by Feature Extraction 10.5.1.1 (Agilent Techinologies). gProcessed signal provided in Processed_data_UiTeiLab190808.txt.

label_protocol: Cy-3 labeled RNA were synthesized by Quick Amp Labeling kit for One color (Agilent Techinologies).

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (Wako) containing 10% fetal bovine serum (Gibco) at 37°C with 5% CO2.

extract_protocol: Total RNAs were extracted by RNeasy mini kit (QIAGEN).

treatment_protocol: Non treated

value: cervical cancer cells

value: HeLa

value: female


title: LGP2KO_SeV

description: Gene expression

value: LGP2 knockout


title: IU301


title: IU302


title: IU502


title: Matrigel_6w_C57BL6_gland1

city: Merelbeke

first: Jonas

last: Steenbrugge

address: Salisburylaan 133

department: Veterinary and Biosciences

institute: Ghent University

data_processing:
Reads were mapped to the mouse reference genome (mm10) using STAR.
Read counts were generated using the summariseOverlaps function from the BioConductor package GenomicAlignments.
Raw counts were normalized and analyzed for differential expression using the DESeq2 package in BioConductor. Regression models were set up to allow evaluation of expression differences between the 4T1 and Py230-based intraductal model at each time point and plain time effects were accounted for using the Matrigel® control samples. Significant differences were considered when nominal P-values were inferior to 5%.
Lists of differentially expressed genes were translated into biological concepts (i.e. hallmark category of the molecular signatures database from the Broad Institute) using gene set enrichment analysis (GSEA). Therefore, mouse gene symbols were first translated into their human homologs using the getLDS function from the biomaRt package in BioConductor.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts, Deseq2 results at every time point, and hallmark categorization

source_name: C57BL/6-derived mammary gland

extract_protocol:
Primary tumors were removed, flash frozen in liquid nitrogen, and RNA was isolated using the Rneasy Mini Kit (QiAgen, Valencia, CA, USA) according to the manufacturer's instructions. 100 ng of total RNA was subjected to a stranded library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: intraductally inoculated material

value: Matrigel®

tag: time post-inoculation

value: 6 weeks


title: Matrigel_6w_C57BL6_gland3


title: Matrigel_1w_C57BL6_gland3

value: 1 week


title: Matrigel_1w_C57BL6_gland2


title: Matrigel_6w_BALBc_gland1

source_name: BALB/c-derived mammary gland

value: BALB/c


title: Matrigel_3w_C57BL6_gland1

value: 3 weeks


title: Matrigel_6w_BALBc_gland3


title: Py230_6w_tumor3

description:
normalized_counts.txt
DESeq_6w.txt
hallmark_categorization.txt

source_name: Py230 tumor

value: Tumor

value: Py230 tumor cells


title: MOLM14.ASLAN_3

description:
AML MOLM14 cell line treated with ASLAN003, replicate 3.
processed data file: JB.Aslan_fpkmlg2.txt


title: Matrigel_3w_BALBc_gland1


title: Matrigel_6w_C57BL6_gland2


title: Matrigel_3w_C57BL6_gland2


title: Matrigel_6w_BALBc_gland2


title: Matrigel_3w_BALBc_gland2


title: Matrigel_3w_C57BL6_gland3


title: Py230_6w_tumor1


title: Py230_6w_tumor2


title: Matrigel_3w_BALBc_gland3


title: Py230_3w_tumor3

description:
normalized_counts.txt
DESeq_3w.txt
hallmark_categorization.txt


title: Matrigel_1w_C57BL6_gland1


title: Py230_3w_tumor2


title: Py230_3w_tumor1


title: Py230_1w_tumor1

description:
normalized_counts.txt
DESeq_1w.txt
hallmark_categorization.txt


title: Py230_1w_tumor3


title: Py230_1w_tumor2


title: 4T1_6w_tumor3

source_name: 4T1 tumor

value: 4T1 tumor cells


title: 4T1_6w_tumor2


title: Matrigel_1w_BALBc_gland2


title: Matrigel_1w_BALBc_gland3


title: Matrigel_1w_BALBc_gland1


title: 4T1_6w_tumor1


title: 4T1_3w_tumor2


title: 4T1_1w_tumor1


title: 4T1_1w_tumor3


title: XCC44

city: Columbus

first: Christopher

middle: C

last: Coss

state: Ohio

address: 496 W. 12th Avenue

department: College of Pharmacy

institute: The Ohio State University

data_processing:
Adaptors were trimmed from raw fastq reads using Trimmomatic verson 0.36
trimmed reads were aligned to mm10 using Subread 1.5.0-p2
duplicate reads were marked with Picard v2.3.0
read counting (paired end) was performed with the summarizeOverlaps function in R (package GenomicAlignments)
differential expression analyses performed with DEseq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts table

source_name: Gastrocnemius

extract_protocol:
Gastrocnemius muscles were removed, flash frozen on in liquid nitrogen, and RNA was harvested using the mirVana™ miRNA Isolation Kit, with phenol (ThermoFisher; Waltham, MA). 600 ng total RNA (Bioanalyzer RIN values > 7) was used to generate polyA enriched RNA-seq libraries with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., catolog number E7760) and sequenced as PE-150 reads on HiSeq 4000 (Illumina Inc, San Diego, CA).
polyA enriched RNA-seq libraries were generated from 600 ng total RNA (RIN > 7) with the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's recommended protocols

tag: tumor

value: Yes

tag: group


title: XCC17

value: No


title: 4T1_3w_tumor1


title: XCC40


title: XCC18


title: XCC48


title: XCC16


title: XCC13


title: XCC20


title: XCC23


title: 4T1_1w_tumor2


title: XCC38


title: XCC39


title: 4T1_3w_tumor3


title: XCC35


title: XCC51


title: XCC28

value: Cx


title: XCC27


title: XCC05


title: XCC47


title: XCC43


title: XCC25


title: XCC62

value: GTx


title: XCC61


title: XCC11


title: XCC02


title: XCC52

value: Ctrl


title: XCC49


title: XCC14


title: XCC01


title: XCC03


title: XCC12


title: XCC42


title: hMeDIP-seq-input

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Library strategy: hMeDIP-seq
RNA-seq: Illumina Casava software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 whole genome by Tophat with default options.
RNA-seq: Reads Per Kilobase of exon per Megabase of library size (RPKM) were detected by DEGseq.
hMeDIP-seq: Illumina Casava software used for basecalling.
hMeDIP-seq: Sequenced reads were trimmed for adaptor sequence.
hMeDIP-seq: After passing Solexa CHASTITY quality filter, the clean reads were aligned to Mus_musculus genome (UCSC MM10) using BOWTIE software (V2.1.0).
hMeDIP-seq: Aligned reads were used for peak calling, both mRNA and LncRNA associated hMeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10-4 by MACS v2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tet1_RNA-seq_exp.txt: Tab-delimited text file contains the estimated expression values produced by DEGseq.
Supplementary_files_format_and_content: *_Mus_musculus_MM10_hisat2_alignment.bed: Bed files were generated by bowtie.

source_name: OPC culture

growth_protocol: Mouse OPCs were isolated from P6 cortices of mice by immunopanning with antibodies against Ran-2, GalC and O4 sequentially. Briefly, cerebral hemispheres were diced and digested with papain at 37°C. Following gentle trituration, cells were resuspended in a panning buffer containing insulin (5 µg/ml) and then incubated at room temperature sequentially on three immunopanning dishes: Ran-2, anti-GalC, and O4. O4+GalC− OPCs were released from the final panning dish with trypsin.

extract_protocol:
Genomic DNA was sonicated to ~200-800bp with a Bioruptor sonicator (Diagenode). 800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol (FC-102-1002, Illumina). After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation (IP) with a mouse monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode, C15200200). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL IP buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 20 μL of magnetic beads were added and incubated for an additional 2 hours at 4°C with agitation. After IP, a total of five washes were performed with ice-cold IP buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. DNA was then purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen).
14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting products were purified with Qiagen MinElute columns, after which a final size selection (300-1,000 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer.

tag: sample type

value: Input

tag: strain/background

tag: cell type

value: Oligodendrocyte progenitor cells


title: RNA-seq-Ctr-2

description:
Con-RNA-2
processed data: Tet1_RNA-seq_exp.txt

data_processing:
RNA-seq: Illumina Casava software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 whole genome by Tophat with default options.
RNA-seq: Reads Per Kilobase of exon per Megabase of library size (RPKM) were detected by DEGseq.
hMeDIP-seq: Illumina Casava software used for basecalling.
hMeDIP-seq: Sequenced reads were trimmed for adaptor sequence.
hMeDIP-seq: After passing Solexa CHASTITY quality filter, the clean reads were aligned to Mus_musculus genome (UCSC MM10) using BOWTIE software (V2.1.0).
hMeDIP-seq: Aligned reads were used for peak calling, both mRNA and LncRNA associated hMeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10-4 by MACS v2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tet1_RNA-seq_exp.txt: Tab-delimited text file contains the estimated expression values produced by DEGseq.
Supplementary_files_format_and_content: *_Mus_musculus_MM10_hisat2_alignment.bed: Bed files were generated by bowtie.

extract_protocol:
RNA from control and Tet1 mutant OPC cultures were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: Control


title: RNA-seq-cKO-2

description:
TET1CKO-OPC2
processed data: Tet1_RNA-seq_exp.txt

value: Mutant


title: RNA-seq-cKO-1

description:
TET1CKO-OPC1
processed data: Tet1_RNA-seq_exp.txt


title: hMeDIP-seq-Ctr-2


title: hMeDIP-seq-cKO-1


title: hMeDIP-seq-Ctr-1


title: hMeDIP-seq-cKO-2


title: XCC07


title: RNA-seq-Ctr-1

description:
Con-RNA-1
processed data: Tet1_RNA-seq_exp.txt


title: huh28_MC-LR_24h_rep3

city: Nanjing

first: Shen

address: Hankou Road 22

institute: nanjing university

description: Gene expression data from huh28 cells treated with MC-LR at 500 nM for 24 h.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

source_name: huh28 cells treated with MC-LR

label_protocol: Total RNA were amplified, labeled and purified followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: huh28 cells were treated with DMEM or MC-LR diluted with DMEM for 24 h.

tag: cell

value: intrahepatic cholangiocarcinoma cell lines


title: huh28_blank_24h_rep3

description: Gene expression data from huh28 cells treated with DMEM only for 24 h.

source_name: huh28 cells treated with DMEM


title: huh28_blank_24h_rep2


title: huh28_MC-LR_24h_rep1


title: huh28_blank_24h_rep1


title: Subject35.W0.LS.Stelara

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: adult with moderate-to-severe atopic dermatitis

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: diagnosis

value: atopic dermatitis

tag: tissue

value: skin

tag: timepoint

value: LS

tag: treatment

value: Ustekinumab

tag: technique

value: Vivo


title: Subject34.W0.LS.Placebo

value: Placebo


title: Subject31.W16.NL.Placebo

value: NL


title: huh28_MC-LR_24h_rep2


title: Subject31.W16.LS.Placebo


title: Subject31.W4.LS.Placebo


title: Subject33.W0.LS.Placebo


title: Subject34.W16.LS.Placebo


title: Subject33.W4.LS.Placebo


title: Subject31.W0.LS.Placebo


title: Subject34.W4.LS.Placebo


title: Subject32.W4.LS.Stelara


title: Subject31.W0.NL.Placebo


title: Subject33.W0.NL.Placebo


title: Subject35.W16.LS.Stelara


title: Subject30.W4.LS.Stelara


title: Subject30.W32.NL.Stelara


title: Subject33.W16.NL.Placebo


title: Subject32.W0.LS.Stelara


title: Subject35.W4.LS.Stelara


title: Subject32.W0.NL.Stelara


title: Subject30.W0.NL.Stelara


title: Subject30.W16.LS.Stelara


title: Subject33.W16.LS.Placebo


title: Subject30.W16.NL.Stelara


title: Subject30.W0.LS.Stelara


title: Subject30.W32.LS.Stelara


title: Subject28.W16.LS.Placebo


title: Subject29.W0.LS.Stelara


title: Subject27.W16.LS.Placebo


title: Subject29.W4.LS.Stelara


title: Subject28.W0.LS.Placebo


title: Subject29.W16.NL.Stelara


title: Subject28.W32.LS.Placebo


title: Subject29.W0.NL.Stelara


title: Subject28.W4.LS.Placebo


title: Subject27.W16.NL.Placebo


title: Subject26.W16.LS.Stelara


title: Subject27.W4.LS.Placebo


title: Subject27.W0.LS.Placebo


title: Subject23.W0.NL.Stelara


title: Subject25.W0.LS.Placebo


title: Subject26.W0.LS.Stelara


title: Subject22.W32.LS.Placebo


title: Subject23.W16.LS.Stelara


title: Subject22.W16.LS.Placebo


title: Subject27.W0.NL.Placebo


title: Subject22.W0.LS.Placebo


title: Subject25.W4.LS.Placebo


title: Subject26.W32.LS.Stelara


title: Subject23.W16.NL.Stelara


title: Subject22.W4.LS.Placebo


title: Subject22.W16.NL.Placebo


title: Subject23.W4.LS.Stelara


title: Subject23.W0.LS.Stelara


title: Subject26.W4.LS.Stelara


title: D32M

city: Camperdown

first: Stuart

middle: J

last: Gallagher

state: NSW

address: Building 93, RPA Hospital

department: Melanoma Oncology

institute: Centenary Institute

data_processing:
Fastq files were checked for quality using Fastqc
Reads were aligned to Human-GRCh38-93 using STAR version 020201, from the Subread package. The genomeGenerate command in STAR was used to build the genome prior to alignment. STAR aligment produced unsorted bam files
BAM files were sorted using the "sort" command in samtools version 1.3.1
Aligned and sorted BAM files were then counted into features at the gene level using featureCounts version 1.5.0-p3 with options "-p -t exon -g gene_id" to generae the CountsTable.csv file
FPKM data was calculated using the fpkm command in the DeSEQ2 package version 1.26.0 in R version 3.5.3
Genome_build: Human-GRCh38-93
Supplementary_files_format_and_content: featurecounts_MelanomaCellLines.csv is counts of the number of fragments  per gene, generated from using the featureCounts tool as above.This data is un-normalised.
Supplementary_files_format_and_content: FPKM_MelanomaCellLines.csv is normalized, FPKM data for each cell line generated using the Deseq2 as above
Supplementary_files_format_and_content: CellLineInformation.csv contains information regardgin each cell line, such as mutations identifed using OncoPrint

source_name: cultured melanoma cells

growth_protocol: Melanoma cells were cultured in RPMI for 48 hours.

extract_protocol:
Total RNA was extracted using RNeasy Mini Plus Kits (Qiagen, Hilden, Germany) with cells being lysed directly in culture flasks
RNA-seq was performed by Macrogen (South Korea) using 100bp paired-end sequencing on a HiSeq 2000 (Illumina)

treatment_protocol: Cells were untreated

tag: passage

value: Passage number <15


title: D38M2


title: D36M


title: D41M


title: D24M


title: Subject21.W16.LS.Stelara


title: Subject21.W0.LS.Stelara


title: D35M1


title: Subject21.W16.NL.Stelara


title: D23M


title: Subject21.W0.NL.Stelara


title: D22M1


title: D20M


title: D11M2


title: D10M


title: D17M1


title: Subject20.W4.LS.Stelara


title: Subject20.W16.LS.Stelara


title: D08M


title: Subject20.W0.LS.Stelara


title: Subject22.W0.NL.Placebo


title: Subject19.W32.NL.Placebo


title: Subject19.W4.LS.Placebo


title: D14M2


title: Subject19.W16.NL.Placebo


title: C106M


title: C100M


title: D04M


title: Subject19.W0.LS.Placebo


title: Subject19.W0.NL.Placebo


title: FLAG-NPM1c expressing ES_anti-FLAG_ChIP

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

data_processing:
Reads were mapped to the humane (resp. mouse) reference genome GRCh38 (resp. GRCm38) using the HISAT software (v2.1.0).
Only unireads were retained and duplicates were removed.
The resulting BAM files were input to the deepTools (v.3.1.3) suite to generate bigWig files in 100bp bins smoothed over 100bp windows with RPKM normalization.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: bigWig files were generated for ChIP-seq signal visualization.

source_name: mouse ES

extract_protocol:
The cross-linked chromatin was sheared by sonication, and MNase treatment.
To repair ChIP-DNA and Input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with Illumina (PCR primer InPE1.0 & InPE2.0).

value: mouse ES

tag: chip antibody

value: FLAG (SIGMA, F1804)


title: C094M


title: Subject21.W4.LS.Stelara


title: FLAG-NPM1 expressing ES_anti-FLAG_ChIP


title: C092M


title: Clone #2-34 ES_anti-FLAG_ChIP


title: Clone #2-2 ES_anti-FLAG_ChIP


title: Subject19.W16.LS.Placebo


title: D05M1


title: Subject18.W32.LS.Placebo


title: FLAG-NPM1c expressing ES_INPUT

description: INPUT for anti-FLAG (SIGMA, F1804) ChIP

value: INPUT


title: Subject18.W16.LS.Placebo


title: Subject18.W4.LS.Placebo


title: FLAG-NPM1 expressing ES_INPUT

description: INPUT for anti-FLAG (SIGMA, F1804) ChIP


title: Subject18.W32.NL.Placebo


title: Subject19.W32.LS.Placebo


title: C091M


title: Subject18.W0.LS.Placebo


title: C089M


title: Subject18.W16.NL.Placebo


title: Subject18.W0.NL.Placebo


title: Clone #2-2 ES_INPUT

description: INPUT for anti-FLAG (SIGMA, F1804) ChIP


title: Clone #2-34 ES_INPUT

description: INPUT for anti-FLAG (SIGMA, F1804) ChIP


title: C088M1


title: 08C_TP_RPL34B

city: College Station

first: Rodolfo

last: Aramayo

state: Texas

address: Room 412, Biological Sciences Building West (BSBW)

department: Biology

institute: Texas A&M University

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 4000 in High Output mode. Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Sequencer .bcl basecall files were de-multiplexed, allowing a 1bp mismatch, and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl. Cutadapt 1.8 was used to identify reads that contained >5bp of sequence adaptor and binned but not processed to remove adaptor.
bowtie-align-s version 1.2.2
RSEM v1.3.1
samtools 1.3
Genome_build: S288C_reference_sequence_R64-2-1_20150113
Supplementary_files_format_and_content: All output files are rsem-calculate-expression output files in text format

organism: Saccharomyces cerevisiae

source_name: Transcriptional_Profile_75 fL

growth_protocol: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

extract_protocol:
We used the same approach we had described previously (Blank et al., 2017), to collect cells from elutriated cultures of each ribosomal protein deletion and generate ribosome footprint libraries. For the RNAseq libraries from the same samples, we also used the same approach we had described (Blank et al., 2017), except that we did not select for polyA-tailed RNAs. Instead, from total RNA, we depleted rRNA, using the ‘Ribo-Zero™ Magnetic Gold Kit (Yeast)’, according to the manufacturer’s instructions.
All RNA-seq libraries were sequenced on an Illumina HiSeq4000, with multiplexing, at the Texas A&M AgriLife Genomics and Bioinformatics Facility
For the ribosome footprint libraries, the cell extracts were prepared as follows: The cell pellets were in 1.5 ml screw-cap microcentrifuge tubes and they were washed once with 1 ml ice-cold DEPC-treated water, centrifuged at 13,000 g for 1 min and the supernatant was aspirated. To each tube we added 0.25 ml glass beads (425-600 μm; Sigma-Aldrich, Cat#: G9268) and 0.4 ml ice-cold lysis buffer, which is described in Ingolia et al (Ingolia et al., 2012). The cells were broken by vortexing at full speed eight times, for 15 sec each time. The samples were placed in ice for at least 30 sec between each vortexing. The extracts were clarified by centrifugation at 5,000 g for 5 min, at 4 °C. The supernatant was clarified in a second centrifugation, at 13,000 g for 10 min, at 4 °C.
All subsequent steps for the ribosome footprint libraries were performed as described in Ingolia et al (Ingolia et al., 2012), except step 7, where we used 1.875 μl of RNase I (100 U μl-1) per reaction. For all gel extractions, we used the overnight protocol described in (Ingolia et al., 2012). Depletion of rRNA was done as described in (Ingolia et al., 2012). In the final PCR amplification and barcode addition step, we amplified each library for 12 cycles

treatment_protocol: We used centrifugal elutriation to isolate growing, highly synchronous, unbudded, early G1 cell populations and scored the elutriated cultures over time microscopically, recording the percentage of budded cells with a particle counter that directly measures their volume (channelyzer). Generation of both the Ribosome Profile (RP) and Transcriptional Profile (TP) libraries require at least ≥2E+09 yeast cells per sample. Such sample size could not be collected following a typical time-series experiment because only a small minority of the total cell population is in early G1 at any given moment. Instead, we allowed the entire cell population of each elutriated fraction to progress in the cell cycle until it reached a given cell size (e.g., 40  fL), at which point the sample was harvested. Elutriated cells of the same size were pooled together until enough cells per sample were obtained. This pool of same-size cells defined one experimental replicate (e.g., Sample01A). We harvested cells with 5 fL cell size increments, from the time they are born (40  fL -- Sample01), until the end of the cell cycle (75  fL -- Sample08)

tag: genotype/variation

tag: ploidy

value: diploid

tag: culture condition

value: 75 fL

tag: experiment type

value: Transcriptional Profiling

tag: molecule subtype

value: PolyA RNA


title: 08B_TP_RPL34B

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: C086M


title: 07C_TP_RPL34B

source_name: Transcriptional_Profile_70 fL

value: 70 fL


title: 08A_TP_RPL34B


title: 07A_TP_RPL34B


title: 07B_TP_RPL34B


title: C084M


title: 06C_TP_RPL34B

source_name: Transcriptional_Profile_65 fL

value: 65 fL


title: Subject17.W16.LS.Stelara

value: atopic dermatitis

value: skin


title: C077M1


title: Subject17.W16.NL.Stelara

value: Ustekinumab


title: Subject17.W4.LS.Stelara

value: LS

value: Vivo


title: Subject29.W16.LS.Stelara


title: C076M


title: C074M


title: 05C_TP_RPL34B

source_name: Transcriptional_Profile_60 fL

value: 60 fL


title: 06A_TP_RPL34B


title: Subject17.W0.NL.Stelara

value: NL


title: 05A_TP_RPL34B


title: 04B_TP_RPL34B

source_name: Transcriptional_Profile_55 fL

value: 55 fL


title: C071M

value: Passage number <15


title: C067M


title: C065M


title: 04A_TP_RPL34B


title: 06B_TP_RPL34B


title: 03A_TP_RPL34B

source_name: Transcriptional_Profile_50 fL

value: 50 fL


title: Subject17.W0.LS.Stelara


title: 04C_TP_RPL34B

value: diploid


title: 02C_TP_RPL34B

source_name: Transcriptional_Profile_45 fL

value: 45 fL


title: 02B_TP_RPL34B

value: Transcriptional Profiling


title: C062M2


title: 05B_TP_RPL34B

value: PolyA RNA


title: Subject16.W32.NL.Stelara


title: Subject16.W20.LS.Stelara


title: Subject16.W32.LS.Stelara


title: 02A_TP_RPL34B

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: Subject16.W16.NL.Stelara


title: Subject16.W4.LS.Stelara


title: 03C_TP_RPL34B


title: C060M


title: Subject16.W16.LS.Stelara


title: 01C_TP_RPL34B

source_name: Transcriptional_Profile_40 fL

value: 40 fL


title: C058M


title: 01B_TP_RPL34B


title: 03B_TP_RPL34B


title: C057M


title: 08C_RP_RPL34B

source_name: Ribosome_Profile_75 fL

value: 75 fL

value: Ribosome Profiling

value: Protected RNA


title: 08B_RP_RPL34B


title: 08A_RP_RPL34B


title: 01A_TP_RPL34B


title: C055M


title: 07C_RP_RPL34B

source_name: Ribosome_Profile_70 fL

value: 70 fL


title: C054M


title: 07A_RP_RPL34B


title: 07B_RP_RPL34B


title: C044M


title: 06C_RP_RPL34B

source_name: Ribosome_Profile_65 fL

value: 65 fL


title: 06B_RP_RPL34B


title: Subject16.W0.NL.Stelara

value: atopic dermatitis

value: skin

value: Ustekinumab

value: Vivo


title: 06A_RP_RPL34B


title: Subject15.W16.LS.Placebo

value: LS

value: Placebo


title: Subject15.W4.LS.Placebo


title: 05A_RP_RPL34B

source_name: Ribosome_Profile_60 fL

value: diploid

value: 60 fL


title: 05B_RP_RPL34B


title: Subject15.W0.LS.Placebo


title: C027M

value: Passage number <15


title: Subject16.W0.LS.Stelara


title: C025M1


title: C037M


title: Subject14.W32.NL.Stelara

value: NL


title: C022M1


title: 04B_RP_RPL34B

source_name: Ribosome_Profile_55 fL

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

value: 55 fL


title: 04A_RP_RPL34B


title: 03B_RP_RPL34B

source_name: Ribosome_Profile_50 fL

value: 50 fL


title: C021M


title: 03C_RP_RPL34B

value: Ribosome Profiling


title: 02C_RP_RPL34B

source_name: Ribosome_Profile_45 fL

value: 45 fL

value: Protected RNA


title: 03A_RP_RPL34B


title: 02B_RP_RPL34B


title: C017M

source_name: cultured melanoma cells


title: 05C_RP_RPL34B


title: Subject14.W32.LS.Stelara

source_name: adult with moderate-to-severe atopic dermatitis


title: Subject14.W16.LS.Stelara


title: Subject14.W16.NL.Stelara


title: 04C_RP_RPL34B


title: Subject14.W20.LS.Stelara


title: C016M


title: C011M


title: C013M


title: 01B_RP_RPL34B

source_name: Ribosome_Profile_40 fL

value: 40 fL


title: Subject14.W4.LS.Stelara

value: atopic dermatitis


title: 02A_RP_RPL34B


title: 08C_TP_RPL34A

source_name: Transcriptional_Profile_75 fL

value: 75 fL

value: Transcriptional Profiling

value: PolyA RNA


title: Subject14.W0.NL.Stelara

value: skin

value: Ustekinumab

value: Vivo


title: C006M


title: Subject14.W0.LS.Stelara

value: LS


title: 08B_TP_RPL34A

value: diploid


title: 07C_TP_RPL34A

source_name: Transcriptional_Profile_70 fL

value: 70 fL


title: 08A_TP_RPL34A

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: 07B_TP_RPL34A


title: Subject13.W20.LS.Stelara


title: C002M

value: Passage number <15


title: C001M


title: 07A_TP_RPL34A


title: 01C_RP_RPL34B


title: 06B_TP_RPL34A

source_name: Transcriptional_Profile_65 fL

value: 65 fL


title: Subject13.W16.NL.Stelara

value: NL


title: A15M2


title: 06C_TP_RPL34A


title: Subject13.W16.LS.Stelara


title: 01A_RP_RPL34B

value: Ribosome Profiling


title: 05C_TP_RPL34A

source_name: Transcriptional_Profile_60 fL

value: 60 fL


title: A11M


title: A06M


title: 05B_TP_RPL34A


title: Subject13.W0.LS.Stelara


title: Subject13.W0.NL.Stelara


title: 04B_TP_RPL34A

source_name: Transcriptional_Profile_55 fL

value: 55 fL


title: A04M


title: 04C_TP_RPL34A


title: 03C_TP_RPL34A

source_name: Transcriptional_Profile_50 fL

value: 50 fL


title: Subject13.W4.LS.Stelara

value: atopic dermatitis


title: 06A_TP_RPL34A

value: Transcriptional Profiling


title: 03A_TP_RPL34A

value: PolyA RNA


title: 03B_TP_RPL34A


title: A02M1


title: Dcdc2a-EGFP/Rpl10a-ES2575 Input4

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: CNS Ventricle

extract_protocol:
The area of the brain surrounding the ventricles was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

tag: molecule type

value: Total RNA

tag: animal line

value: Dcdc2a-TRAP ES2575

value: Input


title: Dcdc2a-EGFP/Rpl10a-ES2575 IP4

value: Ribosomal-bound RNA

tag: sample type

value: Immunopurified (IP)


title: 05A_TP_RPL34A

value: diploid


title: 02C_TP_RPL34A

source_name: Transcriptional_Profile_45 fL

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

value: 45 fL


title: 02B_TP_RPL34A


title: 01B_TP_RPL34A

source_name: Transcriptional_Profile_40 fL

value: 40 fL


title: 01C_TP_RPL34A


title: 04A_TP_RPL34A


title: Subject12.W0.LS.Placebo

value: skin

value: LS

value: Placebo

value: Vivo


title: Subject12.W16.NL.Placebo

value: NL


title: 01A_TP_RPL34A


title: Subject12.W0.NL.Placebo

value: atopic dermatitis


title: Subject12.W16.LS.Placebo


title: Dcdc2a-EGFP/Rpl10a-ES2575 IP3


title: Dcdc2a-EGFP/Rpl10a-ES2575 Input3


title: 02A_TP_RPL34A

value: Transcriptional Profiling


title: Dcdc2a-EGFP/Rpl10a-ES2575 Input1


title: 06C_RP_RPL34A

source_name: Ribosome_Profile_65 fL

value: 65 fL

value: Ribosome Profiling

value: Protected RNA


title: 07A_RP_RPL34A

source_name: Ribosome_Profile_70 fL

value: 70 fL


title: 07B_RP_RPL34A


title: 08C_RP_RPL34A

source_name: Ribosome_Profile_75 fL

value: 75 fL


title: 08B_RP_RPL34A


title: Dcdc2a-EGFP/Rpl10a-ES2575 IP1

value: Ribosomal-bound RNA

value: Dcdc2a-TRAP ES2575

value: Immunopurified (IP)


title: 08A_RP_RPL34A

value: diploid

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: Subject11.W32.LS.Stelara

value: skin

value: Ustekinumab


title: 05C_RP_RPL34A

source_name: Ribosome_Profile_60 fL

value: 60 fL


title: 06A_RP_RPL34A


title: Subject12.W4.LS.Placebo

value: LS

value: Placebo

value: Vivo


title: Subject11.W0.LS.Stelara

value: atopic dermatitis


title: 05A_RP_RPL34A


title: 05B_RP_RPL34A


title: Subject10.W20.LS.Placebo


title: Dcdc2a-EGFP/Rpl10a-ES2575 Input2

value: Total RNA

value: Input


title: Subject11.W20.LS.Stelara


title: IEL18_1_5

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: library of 96 wt IELP cells

growth_protocol: Mice were housed under SPF condition at the department of medical microbiology and hygiene of the university medical center Freiburg in accordance with the local animal care committiees and Regierungspräsidium Freiburg

extract_protocol:
IELPs were isolated by dissecting the thymus and single cell suspension of the thymus was isolated by mashing the tissue through a 70µm cell strainer with 15ml PBS. Lymphocytes were enriched by performing red cell lysis and IELPs were enriched by depleting CD4+ and CD8+ thymocytes by incubation with anti-CD4 and anti-CD8 purified antibodies and anti-mouse Dynabeads.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: strain background

value: TBGR

value: wild type

tag: age

value: 4 wk

value: Thymus

tag: cell type

value: intraepithelial lymphocytes (IELs)


title: IEL18_2_6

tag: tissue


title: 06B_RP_RPL34A

tag: timepoint

value: 65 fL

value: Ribosome Profiling

value: Protected RNA


title: 07C_RP_RPL34A

value: diploid

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

value: 70 fL


title: IEL17_1_7


title: IEL_16_2


title: IEL17_2_8


title: 01C_RP_RPL34A

value: 40 fL


title: 03C_RP_RPL34A

source_name: Ribosome_Profile_50 fL

value: 50 fL


title: 02C_RP_RPL34A

source_name: Ribosome_Profile_45 fL

value: 45 fL


title: 04B_RP_RPL34A

source_name: Ribosome_Profile_55 fL

value: 55 fL


title: 04C_RP_RPL34A


title: 02A_RP_RPL34A


title: 03B_RP_RPL34A


title: 03A_RP_RPL34A


title: 04A_RP_RPL34A


title: 01A_RP_RPL34A

source_name: Ribosome_Profile_40 fL


title: 02B_RP_RPL34A


title: IEL_15_1


title: IEL_15_2


title: IEL_16_1


title: Subject11.W16.LS.Stelara

source_name: adult with moderate-to-severe atopic dermatitis

tag: diagnosis

value: atopic dermatitis

value: skin

value: LS

tag: treatment

value: Ustekinumab

value: Vivo


title: 01B_RP_RPL34A


title: Subject11.W4.LS.Stelara

tag: technique


title: 08C_TP_RPL22B

source_name: Transcriptional_Profile_75 fL

value: 75 fL

value: Transcriptional Profiling

value: PolyA RNA


title: Subject10.W0.LS.Placebo

value: Placebo


title: Hdc_gfplo HSC sample_4

first: Timothy

middle: Cragin

last: Wang

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

description: xm0048_GFPlo HSC_04

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file with raw counts for each gene

source_name: Hdc-GFPlo HSC cells

extract_protocol:
Total RNA was isolated from sorted 500 Hematopoetic Stem Cells using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.

value: Hdc-GFPlo

value: bone marrow

value: hematopoetic stem cells (HSCs)

tag: sorted fraction

value: Hdc-GFP-


title: 08B_TP_RPL22B

tag: genotype/variation

value: diploid

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: Subject10.W4.LS.Placebo


title: Subject8.W32.LS.Placebo


title: Hdc_gfplo HSC sample_2

description: xm0046_GFPlo HSC_02

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file with raw counts for each gene

source_name: Hdc-GFP HSC cells


title: 07B_TP_RPL22B

source_name: Transcriptional_Profile_70 fL

tag: ploidy

value: 70 fL


title: 07C_TP_RPL22B

tag: culture condition


title: 05C_TP_RPL22B

source_name: Transcriptional_Profile_60 fL

value: 60 fL

tag: experiment type


title: 08A_TP_RPL22B

tag: molecule subtype


title: Hdc_gfphi HSC sample_3

value: Hdc-GFPhi


title: 05B_TP_RPL22B


title: 06A_TP_RPL22B

source_name: Transcriptional_Profile_65 fL

value: 65 fL


title: Hdc_gfplo HSC sample_1

description: xm0045_GFPlo HSC_01

extract_protocol:
Total RNA was isolated from sorted 500Hematopoetic Stem Cells using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.


title: 06B_TP_RPL22B


title: 06C_TP_RPL22B


title: Subject10.W16.LS.Placebo

value: atopic dermatitis

value: skin

value: LS


title: Subject8.W4.LS.Placebo

value: Vivo


title: 04C_TP_RPL22B

source_name: Transcriptional_Profile_55 fL

value: 55 fL

value: Transcriptional Profiling


title: 04B_TP_RPL22B

value: PolyA RNA


title: 05A_TP_RPL22B


title: Hdc_gfphi HSC sample_2


title: Subject7.W4.LS.Stelara

value: Ustekinumab


title: 07A_TP_RPL22B


title: Hdc_gfplo HSC sample_3

description: xm0047_GFPlo HSC_03

value: Hdc-GFPlo

value: bone marrow


title: Subject8.W0.LS.Placebo

value: Placebo


title: Subject8.W16.LS.Placebo


title: Subject8.W20.LS.Placebo


title: Subject7.W0.NL.Stelara

value: NL


title: Subject7.W0.LS.Stelara


title: Subject5.W16.LS.Placebo


title: Subject5.W32.LS.Placebo


title: Subject5.W32.NL.Placebo


title: 04A_TP_RPL22B

value: diploid

value: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)


title: Subject5.W20.LS.Placebo


title: 03C_TP_RPL22B

source_name: Transcriptional_Profile_50 fL

value: 50 fL


title: 03B_TP_RPL22B


title: 03A_TP_RPL22B